diff --git a/scripts/grt/export.py b/scripts/grt/export.py index 0a8c3f9e2b2..9e0e1ff7c36 100644 --- a/scripts/grt/export.py +++ b/scripts/grt/export.py @@ -21,6 +21,7 @@ import galaxy.config from galaxy.objectstore import build_object_store_from_config from galaxy.util import hash_util from galaxy.util.script import app_properties_from_args, populate_config_args +from galaxy.util import unicodify sample_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml.sample')) default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), 'grt.yml')) @@ -155,16 +156,15 @@ def main(argv): continue try: - handle_job.write(str(job[0])) # id - handle_job.write('\t') - handle_job.write(job[2]) # tool_id - handle_job.write('\t') - handle_job.write(job[3]) # tool_version - handle_job.write('\t') - handle_job.write(job[4]) # state - handle_job.write('\t') - handle_job.write(str(job[5])) # create_time - handle_job.write('\n') + line = [ + str(job[0]), # id + job[2], # tool_id + job[3], # tool_version + job[4], # state + str(job[5]) # create_time + ] + cline = unicodify('\t'.join(line) + '\n') + handle_job.write(cline.encode('utf-8')) except Exception: logging.warning("Unable to write out a 'handle_job' row. Ignoring the row.", exc_info=True) continue @@ -241,18 +241,16 @@ def main(argv): continue try: - handle_datasets.write(str(job[0])) - handle_datasets.write('\t') - handle_datasets.write(str(hda_id)) - handle_datasets.write('\t') - handle_datasets.write(str(hdas[hda_id][1])) - handle_datasets.write('\t') - handle_datasets.write(round_to_2sd(datasets[dataset_id][0])) - handle_datasets.write('\t') - handle_datasets.write(str(job[2])) - handle_datasets.write('\t') - handle_datasets.write(str(filetype)) - handle_datasets.write('\n') + line = [ + str(job[0]), # Job ID + str(hda_id), # HDA ID + str(hdas[hda_id][1]), # Extension + round_to_2sd(datasets[dataset_id][0]), # File size + job[2], # Parameter name + str(filetype) # input/output + ] + cline = unicodify('\t'.join(line) + '\n') + handle_datasets.write(cline.encode('utf-8')) except Exception: logging.warning("Unable to write out a 'handle_datasets' row. Ignoring the row.", exc_info=True) continue @@ -276,14 +274,15 @@ def main(argv): continue try: - handle_metric_num.write(str(metric[0])) - handle_metric_num.write('\t') - handle_metric_num.write(metric[1]) - handle_metric_num.write('\t') - handle_metric_num.write(metric[2]) - handle_metric_num.write('\t') - handle_metric_num.write(str(metric[3])) - handle_metric_num.write('\n') + line = [ + str(metric[0]), + metric[1], + metric[2], + str(metric[3]) + ] + + cline = unicodify('\t'.join(line) + '\n') + handle_metric_num.write(cline.encode('utf-8')) except Exception: logging.warning("Unable to write out a 'handle_metric_num' row. Ignoring the row.", exc_info=True) continue @@ -303,7 +302,7 @@ def main(argv): os.unlink(REPORT_BASE + '.' + name + '.tsv') _times.append(('job_finish', time.time() - _start_time)) - sha = hash_util.memory_bound_hexdigest(hash_util.sha256, REPORT_BASE + ".tar.gz") + sha = hash_util.memory_bound_hexdigest(hash_func=hash_util.sha256, path=REPORT_BASE + ".tar.gz") _times.append(('hash_finish', time.time() - _start_time)) # Now serialize the individual report data.